Table 1.
Overall prevalence of respiratory viruses, bacteria and Pneumocystis jirovecii among participants
| Respiratory pathogen | Paired cohort |
Nonpaired cohort |
|||||
|---|---|---|---|---|---|---|---|
| Arrival, n (%) of positive specimens | Departure, n (%) of positive specimens | p | Acquisition rate, n (%) positive specimens at departure among individuals negative at arrival | Arrival, n (%) of positive specimens | Departure, n (%) of positive specimens | p | |
| Viruses | |||||||
| Influenza virus A/H3N2 | 4 (0.6%) | 14 (2.0%) | 0.71 | 13 (1.9%) | 6 (1.2%) | 8 (1.7%) | 0.48 |
| Influenza virus 2009 A(H1N1) | 1 (0.1%) | 11 (1.6%) | 0.32 | 10 (1.4%) | 1 (0.2%) | 14 (3.0%) | <0.001 |
| Influenza virus B | 0 | 0 | — | 0 | 0 | 1 (0.2%) | 0.48 |
| Influenza virus C | 0 | 0 | — | 0 | 0 | 0 | — |
| Human parainfluenza viruses 1 | 0 | 0 | — | 0 | 2 (0.4%) | 0 | 0.50 |
| Human parainfluenza viruses 2 | 0 | 2 (0.3%) | — | 2 (0.3%) | 1 (0.2%) | 2 (0.4%) | 0.61 |
| Human parainfluenza viruses 3 | 2 (0.3%) | 1 (0.1%) | — | 1 (0.1%) | 0 | 1 (0.2%) | 0.61 |
| Human parainfluenza viruses 4 | 0 | 1 (0.1%) | — | 1 (0.1%) | 1 (0.2%) | 0 | 1 |
| MERS coronavirus | 0 | 0 | — | 0 | 0 | 0 | — |
| Human coronavirus 229E | 6 (0.9%) | 101 (14.6%) | <0.001 | 101 (14.6%) | 5 (1.0%) | 48 (10.2%) | <0.001 |
| Human coronavirus NL63 | 2 (0.3%) | 14 (2.0%) | 0.71 | 13 (1.9%) | 0 | 1 (0.2%) | 0.48 |
| Human coronavirus HKU1 | 3 (0.4%) | 9 (1.3%) | 0.16 | 9 (1.3%) | 1 (0.2%) | 7 (1.5%) | 0.03 |
| Human coronavirus OC43 | 1 (0.1%) | 11 (1.6%) | 0.34 | 11 (1.6%) | 2 (0.4%) | 9 (1.9%) | 0.02 |
| Human cytomegalovirus | 0 | 0 | — | 0 | 0 | 0 | — |
| Human enterovirus | 4 (0.6%) | 3 (0.4%) | — | 3 (0.4%) | 4 (0.8%) | 5 (1.1%) | 0.74 |
| Human metapneumovirus | 0 | 1 (0.1%) | — | 1 (0.1%) | 1 (0.2%) | 3 (0.6%) | 0.35 |
| Human respiratory syncytial virus | 4 (0.6%) | 5 (0.7%) | — | 5 (0.7%) | 3 (0.6%) | 1 (0.2%) | 0.63 |
| Human rhinovirus | 15 (2.2%) | 238 (34.4%) | <0.001 | 236 (34.1%) | 16 (3.1%) | 145 (30.9%) | <0.001 |
| Human adenovirus | 0 | 4 (0.6%) | — | 4 (0.6%) | 0 | 2 (0.4%) | 0.23 |
| Human bocavirus | 1 (0.1%) | 0 | — | 0 | 1 (0.2%) | 0 | 1 |
| Parechovirus | 0 | 1 (0.1%) | — | 1 (0.1%) | 0 | 0 | — |
| At least one virus | 42 (6.1%) | 343 (49.6%) | <0.001 | 340 (49.1%) | 44 (8.6%) | 212 (45.1%) | <0.001 |
| Bacteria | |||||||
| Bordetella pertussis | 0 | 0 | — | 0 | 0 | 0 | — |
| Mycoplasma pneumoniae | 0 | 0 | — | 0 | 0 | 0 | — |
| Neisseria meningitidis | 0 | 2 (0.3%) | — | 2 (0.3%) | 0 | 3 (0.6%) | 0.11 |
| Streptococcus pneumoniae | 39 (5.6%) | 88 (12.7%) | <0.001 | 83 (12.0%) | 24 (4.7%) | 64 (13.6%) | <0.001 |
| Streptococcus pyogenes | 0 | 0 | — | 0 | 0 | 0 | — |
| Klebsiella pneumoniae | 20 (2.9%) | 27 (3.9%) | 0.09 | 27 (3.9%) | 24 (4.7%) | 26 (5.5%) | 0.54 |
| Legionella pneumophila | 0 | 0 | — | 0 | 0 | 0 | — |
| Salmonella spp. | 0 | 0 | — | 0 | 0 | 0 | — |
| Staphylococcus aureus | 39 (5.6%) | 55 (7.9%) | <0.001 | 52 (7.5%) | 32 (6.2%) | 46 (9.8%) | 0.04 |
| Coxiella burnetii | 0 | 1 (0.1%) | — | 1 (0.1%) | 0 | 0 | — |
| Chlamydophila pneumoniae | 0 | 0 | — | 0 | 0 | 0 | — |
| Haemophilus influenzae | 16 (2.3%) | 81 (11.7%) | <0.001 | 79 (11.4%) | 12 (2.3%) | 67 (14.3%) | <0.001 |
| At least one bacteria | 101 (14.6%) | 201 (29.0%) | <0.001 | 196 (28.3%) | 83 (16.1%) | 158 (33.6%) | <0.001 |
| Pneumocystis jirovecii | 0 | 0 | — | 0 | 0 | 0 | — |
| At least one pathogen | 136 (19.7%) | 430 (62.1%) | <0.001 | 425 (61.4%) | 121 (23.5%) | 306 (65.1%) | <0.001 |